- Avoid overengineering datastructures. Tuples are better than objects (try namedtuple too though). Prefer simple fields over getter/setter functions.
- Built-in datatypes are your friends. Use more numbers, strings, tuples, lists, sets, dicts. Also check out the collections library, esp. deque.
- Be suspicious of function/method calls; creating a stack frame is expensive.
- Are you sure it's too slow? Profile before optimizing!
- The universal speed-up is rewriting small bits of code in C. Do this only when all else fails.
Where does this ATP come from? It is synthesized by an incredibly sophisticated molecular machine, the ATP synthase, embedded in the inner membrane of our mitochondria. Energy from the oxidation of food results in protons being pumped across the membrane to create a proton gradient. The protons drive the rotation of a circular ring of proteins in the membrane that in turn move a central shaft. The shaft interacts sequentially with one of 3 catalytic sites within a hexamer, making ATP (little butterflies in the movie!). The ATP synthase rotates about 150 times/second
To visualize the rotation under a microscope, a very long fluorescent rod (actin filament) was chemically attached to the central shaft. Watch real movies (not animations!) of the enzyme spinning here: http://www.k2.phys.waseda.ac.jp/F1movies/F1long.htm
Notice the rotation is slower with longer rods. The rotor produces a torque of 40 pN nm (40 pico Newtons x nanometer), irrespective of the load. This would be the force you would need to rotate a 500 m long rod while standing at the bottom of a large swimming pool at the rate shown in the movie.
How did this amazing rotor evolve? The hexameric structure is related to DNA helicases that rotate along the DNA double helix, using ATP to unzip the two strands apart. The H+ motor has precedence in flagella motors that use proton gradients to drive rotation of long filaments, allowing bacteria to tumble through their surroundings. At some point, a H+ driven motor came together with a helicase like hexamer to create a rotor driving the hexamer in reverse, to synthesize ATP.
The 1997 Nobel prize in Chemistry was awarded to John Walker and Paul Boyer for solving the structure and cyclical mechanism of the ATP synthase, respectively. This amazing enzyme was also the subject of my own Ph.D. thesis, and my first love!
For #ScienceSunday curated by and .
- Parse.lySoftware Engineer, 2011 - present
- Aleph PointLead Engineer, 2010 - 2011
- Thermo Fisher ScientificSoftware Engineer, 2007 - 2010
- The Neat CompanySoftware-Research Engineer, 2006 - 2007
- Case Western Reserve UniversityComputer Science BS/MS, 2001 - 2006
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